Replays showed that Aubameyang had strayed beyond the last defender before firing past Jordan Pickford, and Silva felt aggrieved with the quality of officiating.
"It was offside. At this level, with these mistakes from the referee, it put our team in that condition as well," he told Sky Sports.
"The second goal is clearly offside. It is really frustrating, and I tell you why. In that moment we had just one player in our box, it is too clear for the assistant.
"It was two or three against one, just Jonjoe Kenny inside the box. It is clear where he is, and where the player who scored is.
"It is clearly offside. For me it is a little bit strange, but OK, mistakes are made, I make them as well, and the assistant and ref they can make them as well."
Silva was, however, satisfied with his team's efforts, insisting that Gunners goalkeeper Petr Cech was the best player on the pitch.
"The result didn't reflect what both teams played during the match. I think we deserved more. We came here to play and challenge the opponents. In the first half we created clear chances," he added.
"Petr Cech was the best player on the pitch, clearly. We didn't deserve this result, our team worked hard to achieve a different result.
"It is a disappointing result for us. But it is football. We created three, four, five clear chances to score. In one detail, a great moment from Lacazette, it changed a little bit the game."